Improve parameter descriptions

soedinglab · Feb 17, 2021 · 228b9e5 · 228b9e5
1 parent 7155316
commit 228b9e5
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
@@ -68,9 +68,9 @@ class LocalParameters : public Parameters {
         PARAM_FDR_CUTOFF(PARAM_FDR_CUTOFF_ID,"--fdr", "FDR cutoff", "FDR cutoff for filtering matches [0.0, 1.0]", typeid(float), (void *) &fdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_TAX_FDR_CUTOFF(PARAM_TAX_FDR_CUTOFF_ID,"--tax-fdr", "Taxonomy FDR cutoff", "FDR cutoff for taxonomy report [0.0, 1.0]", typeid(float), (void *) &taxFdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_FORMAT_TYPE(PARAM_FORMAT_TYPE_ID,"--fmt", "Output format", "0: short (only matches)\n1: long (matches and hits)\n2: long with nucleotide alignment", typeid(int), (void *) &formatType, "^[0-2]{1}$"),
-        PARAM_REPORT_PAM(PARAM_REPORT_PAM_ID,"--report-pam", "Report PAM", "Report protospacer adjacent motifs up and downstream of hits [0,1]", typeid(int), (void *) &reportPam, "^[0-1]{1}$"),
+        PARAM_REPORT_PAM(PARAM_REPORT_PAM_ID,"--report-pam", "Report PAM", "Report protospacer adjacent motifs up and downstream of hits", typeid(int), (void *) &reportPam, "^[0-1]{1}$"),
         PARAM_FLANKING_SEQ_LEN(PARAM_FLANKING_SEQ_LEN_ID,"--flanking-seq-len", "Flanking sequence length", "Length of protospacer flanking sequence to extract for possible PAMs scanning", typeid(int), (void *) &flankingSeqLen, "^[0-9]{1}[0-9]*$"),
-        PARAM_PERFORM_NUCLALN(PARAM_PERFORM_NUCLALN_ID,"--perform-nucl-aln", "Perform nucl-nucl alignment", "Perform a nucl-nucl alignment in addition to the hits reported in 6-frame translated search, and assign the smallest E-value between the two alignments [0,1]", typeid(int), (void *) &performNuclAln, "^[0-1]{1}$"),
+        PARAM_PERFORM_NUCLALN(PARAM_PERFORM_NUCLALN_ID,"--perform-nucl-aln", "Perform nucl-nucl alignment", "0: perform only 6-frame translated search, 1:perform additional nucl-nucl alignment to the hits reported in 6-frame translated search, and update the E-value", typeid(int), (void *) &performNuclAln, "^[0-1]{1}$"),
         PARAM_RESTRICT_RANKS_MODE(PARAM_RESTRICT_RANKS_MODE_ID, "--restrict-ranks-mode", "Rank restriction mode", "0: disabled, 1: restrict taxonomic rank on target prediction by sequence identity", typeid(int), (void *) &restrictRanksMode, "^[0-1]{1}$"),
         PARAM_RANK_MIN_SEQ_IDS(PARAM_RANK_MIN_SEQ_IDS_ID, "--rank-min-seq-ids", "Rank restriction seq.ids.", "Comma-separated sequence identity thresholds to restrict ranks to:\nspecies, genus, family, order, class, phylum, kingdom, superkingdom", typeid(std::string), (void *) &rankMinSeqIds, "")
     {